CRAN Package Check Results for Package compareGroups

Last updated on 2020-06-03 12:49:03 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 4.4.1 23.49 220.47 243.96 OK
r-devel-linux-x86_64-debian-gcc 4.4.1 21.02 162.80 183.82 OK
r-devel-linux-x86_64-fedora-clang 4.4.1 315.91 NOTE
r-devel-linux-x86_64-fedora-gcc 4.4.1 288.99 OK
r-devel-windows-ix86+x86_64 4.4.1 81.00 420.00 501.00 OK
r-patched-linux-x86_64 4.4.1 23.71 214.39 238.10 OK
r-patched-solaris-x86 4.4.1 461.90 NOTE
r-release-linux-x86_64 4.4.1 23.01 214.74 237.75 OK
r-release-osx-x86_64 4.4.1 WARN
r-release-windows-ix86+x86_64 4.4.1 53.00 286.00 339.00 OK
r-oldrel-osx-x86_64 4.4.1 NOTE
r-oldrel-windows-ix86+x86_64 4.4.1 47.00 249.00 296.00 OK

Check Details

Version: 4.4.1
Check: installed package size
Result: NOTE
     installed size is 5.0Mb
     sub-directories of 1Mb or more:
     doc 2.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86

Version: 4.4.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘compareGroups_vignette.Rmd’ using rmarkdown
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Loading required package: SNPassoc
    Loading required package: haplo.stats
    Loading required package: survival
    Loading required package: mvtnorm
    Loading required package: parallel
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     variable 'age7gr' converted to factor since few different values contained
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in norm.plot(x = x.var, file = file.i, var.label.x = var.labels[i], :
     p-value for normality in Age could not be calculated
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compareGroups.fit(X = X, y = y, include.label = include.label, :
     variables tovent specified in 'method' not found
    Warning in cor.test.default(x, as.integer(y), method = "spearman") :
     Cannot compute exact p-value with ties
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in chisq.test(xx, correct = FALSE) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(xx, correct = FALSE) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(xx, correct = FALSE) :
     Chi-squared approximation may be incorrect
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'smk' are removed since no observation in that/those levels
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor(as.integer(x), as.integer(y)) :
     the standard deviation is zero
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'sex' are removed since no observation in that/those levels
    Warning in cor(as.integer(x), as.integer(y)) :
     the standard deviation is zero
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'smk' are removed since no observation in that/those levels
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'smk' are removed since no observation in that/those levels
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'smk' are removed since no observation in that/those levels
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'smk' are removed since no observation in that/those levels
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor(as.integer(x), as.integer(y)) :
     the standard deviation is zero
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in cor(as.integer(x), as.integer(y)) :
     the standard deviation is zero
    Warning in cor(as.integer(x), as.integer(y)) :
     the standard deviation is zero
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'year' are removed since no observation in that/those levels
    Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], :
     Some levels of 'sex' are removed since no observation in that/those levels
    Warning in fitter(X, Y, istrat, offset, init, control, weights = weights, :
     Loglik converged before variable 3 ; coefficient may be infinite.
    Warning in fitter(X, Y, istrat, offset, init, control, weights = weights, :
     Loglik converged before variable 2 ; coefficient may be infinite.
    Warning in fitter(X, Y, istrat, offset, init, control, weights = weights, :
     Loglik converged before variable 2 ; coefficient may be infinite.
    Warning in fitter(X, Y, istrat, offset, init, control, weights = weights, :
     Loglik converged before variable 2 ; coefficient may be infinite.
    Warning in fitter(X, Y, istrat, offset, init, control, weights = weights, :
     Loglik converged before variable 2 ; coefficient may be infinite.
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in HWChisq(X[i, ], ...) :
     Expected counts below 5: chi-square approximation may be incorrect
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in HWChisq(X[i, ], ...) :
     Expected counts below 5: chi-square approximation may be incorrect
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in HWChisq(X[i, ], ...) :
     Expected counts below 5: chi-square approximation may be incorrect
    Warning in HWf(X) : Monomorphic marker, f set to zero.
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in HWChisq(X[i, ], ...) :
     Expected counts below 5: chi-square approximation may be incorrect
    Warning in HWf(X) : Monomorphic marker, f set to zero.
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in homozyg(X) :
     Genotypes are not labelled, default labels (AA, AB, BB) assumed.
    Warning in heterozyg(X) :
     Genotypes are not labelled, default labels assumed.
    Warning in HWChisq(X[i, ], ...) :
     Expected counts below 5: chi-square approximation may be incorrect
    Warning in HWf(X) : Monomorphic marker, f set to zero.
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    Warning in base::deparse(e, width) :
     invalid 'cutoff' value for 'deparse', using default
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'compareGroups_vignette.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘compareGroups_vignette.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘compareGroups_vignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 4.4.1
Check: dependencies in R code
Result: NOTE
    No protocol specified
    No protocol specified
Flavor: r-oldrel-osx-x86_64